Saudi Arabia is facing an international outcry and accusations of promoting sectarian hatred after a Shia Muslim religious leader from the country’s volatile eastern province was sentenced to death.

Sheikh Nimr Baqir al-Nimr, who led protests in Qatif at the height of the Arab spring in 2011, was convicted on Wednesday of sedition and other charges in a case that has been followed closely by Shias in the kingdom and neighbouring Bahrain.

Shia Muslims make up 10%-15% of the population of Sunni-ruled Saudi Arabia, which bills itself as playing a lead role in the fight against the jihadis of Islamic State (Isis) in Syria and Iraq. Riyadh has supported Sunni groups fighting to overthrow Bashar al-Assad but denies backing Isis.

State prosecutors had reportedly asked for Nimr to be crucified. The sentence is thought likely to be commuted on appeal.

Nimr was arrested in 2012 and ill-treated during his two-year detention, much of it spent in solitary confinement. He was denied surgery for bullet wounds suffered when he was arrested. He was charged with “disobeying the ruler”, “inciting sectarian strife”, and encouraging and leading demonstrations.

In Iran, Saudi Arabia’s chief regional rival and the political centre of the Shia world, the foreign ministry warned on Thursday that execution would have “dire consequences”. It called Nimr an ayatollah, giving him the second most senior clerical title in the Shia hierarchy. Iran, like Saudi Arabia, uses capital punishment.

In London the Foreign Office stated that it was aware of the sentencing, adding: “The UK opposes the death penalty as a matter of principle.”

The Saudi authorities have portrayed the cleric as an “instigator of discord and rioting”. But Nimr’s supporters and family have denied that he incited violence.

In a BBC interview, Nimr said he backed “the roar of the word against authorities rather than weapons”. The arrest of his brother and other relatives after sentencing has fuelled anger that is being ventilated on Twitter and other social media.

“Saudi Arabia’s harsh treatment of a prominent Shia cleric is only adding to existing sectarian discord and unrest,” said Joe Stork, deputy Middle East director at Human Rights Watch. “Saudi Arabia’s path to stability in the eastern province lies in ending systematic discrimination against Shia citizens, not in death sentences.”

Amnesty International described Nimr’s sentencing as part of a wider Saudi government crackdown on dissent.

Shia and Sunni groups said they were extremely alarmed by the sentence. “Ayatollah al-Nimr is a respected Muslim figure in Saudi Arabia,” 10 organisations said in statement. “He is a faith leader, reformist and human rights activist, who has campaigned for an end to discriminatory laws against the Shia minority. The sentencing will further inflame sectarian tensions and provide encouragement to extremist groups such as Isis to continue their persecution of religious minorities.”

Toby Matthiesen, a Cambridge expert on Saudi Arabia, said: “In the last two years Nimr has become known by Shia across the world. For many Salafis and Sunnis with anti-Shia leanings he has become a real hate figure. In the context of Isis, the Saudi royal family is trying to legitimise itself in the eyes of Sunnis by being tough. Nimr was a revolutionary who called for non-violent protests and the downfall of the Al Saud, but also for Assad to go. He wasn’t sectarian.”

Yusif al-Khoei, of the London-based Al-Khoei Foundation, said he was “appalled” by the news and with others was considering boycotting a Saudi-organised conference on inter-religious dialogue in Vienna.

• This article was amended on 17 October 2014 to correct the spelling of Toby Matthiesen’s surname and to clarify the quote from him at his request.